Molecular dynamic simulations of Co(III) and Ru(II) polypyridyl complexes and docking studies with dsDNA

The binding studies of Co(III) and Ru(II) polypyridyl complexes with dsDNA were carried out by molecular modeling studies to identify the binding interactions. The 3D structures of the metal complexes [Ru(phen)(2)ippip](2+) (RP-ippip), [Co(phen)(2)ippip](3+) (CP-ippip), [Ru(bpy)(2)ippip](2+) (RB-ippip), and [Co(bpy)(2)ippip](3+) (CB-ippip), where ippip = 4-(isopropylbenzaldehyde)imidazo[4,5-f][1,10] phenanthroline, phen = 1,10-phenanthroline, and bpy = bypyridine, were simulated using molecular dynamic simulations for stable conformers. The energy-minimized 3D structures of metal complexes were docked to the double-stranded dodecamer 5'-D(*AP * CP * CP * GP * AP * CP * GP * TP * CP * GP * GP * T)-3'. The aromatic ligand, ippip, facilitates the binding of the metal complex with DNA through intercalation. The effect of ancillary ligands, phen and bpy, was investigated. The ancillary ligands were found to be involved in bond formation with the phosphate backbone of nucleotide base pairs in metal complex-DNA docked complex. The significant interactions of metal complexes in the major groove of DNA are the prerequisite features of the metal complexes to be considered as DNA-intercalator. The molecular docking data are well substantiated by the available experimental data. The modeling results should extend knowledge about the nature of binding of these complexes with DNA.